rs10957875

Variant names:

• chr8-77910736-G-A
• rs10957875
• ENST00000730975.1:n.479-20437C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-77910736-G-A
• chr8-77910736-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000730975.1(ENSG00000295568):​n.479-20437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,348 control chromosomes in the GnomAD database, including 14,969 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (14969 hom., cov: 31)
• Consequence: ENSG00000295568 ENST00000730975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 0 publications found

Genes affected

ENSG00000295568 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295568	ENST00000730975.1	n.479-20437C>T		intron_variant	Intron 3 of 4
ENSG00000295568	ENST00000730976.1	n.429-20437C>T		intron_variant	Intron 2 of 2
ENSG00000295568	ENST00000730977.1	n.504-20437C>T		intron_variant	Intron 2 of 2
ENSG00000295568	ENST00000730978.1	n.361-897C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66163 AN: 151230 Hom.: 14955 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.458

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.437 AC: 66212 AN: 151348 Hom.: 14969 Cov.: 31 AF XY: 0.441 AC XY: 32585 AN XY: 73940

African (AFR) AF: 0.342 AC: 14163 AN: 41360

American (AMR) AF: 0.498 AC: 7545 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1642 AN: 3456

East Asian (EAS) AF: 0.513 AC: 2626 AN: 5120

South Asian (SAS) AF: 0.458 AC: 2208 AN: 4820

European-Finnish (FIN) AF: 0.471 AC: 4957 AN: 10532

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.468 AC: 31632 AN: 67620

Other (OTH) AF: 0.459 AC: 966 AN: 2106

Alfa AF: 0.463 Hom.: 23756

Bravo AF: 0.438

Asia WGS AF: 0.453 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.63
PhyloP100		-0.013

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10957875; hg19: chr8-78822971;